Osteogenic differentiation of various adult stem cell populations such as neural crest-derived stem cells is of great interest in context of bone regeneration. Ideally, exogenously differentiation should mimic endogenous differentiation process, which is partly mediated by topological cues. To elucidate the osteoinductive potential of porous substrates with different pore diameters (30 nm, 100 nm), human neural crest-derived stem cells isolated from the inferior nasal turbinate were cultivated on the surface of nanoporous titanium covered membranes without additional chemical or biological osteoinductive cues. As controls, flat titanium without any topological features and osteogenic medium was used. Cultivation of human neural crest-derived stem cells on 30 nm pores resulted in osteogenic differentiation as demonstrated by alkaline phosphatase activity after seven days as well as by calcium deposition after 3 weeks of cultivation. In contrast, cultivation on flat titanium and membranes with 100 nm pores was not sufficient to induce osteogenic differentiation. Moreover, we demonstrate increase of osteogenic transcripts including Osterix, Osteocalcin and up-regulation of Integrin β1 and α2 in 30 nm pore approach only. Thus, transplantation of stem cells pre-cultivated on nanostructured implants might improve the clinical outcome by support of the graft adherence and acceleration of the regeneration process.